tbuckley/cabot-search huggingface dataset:
Abstract 4251: Development and characterization of an epiregulin antibody-drug conjugate for targeting colorectal cancer cell plasticity
Authors: Joan Jacob, Zhengdong Liang, Kendra Carmon
Journal: Cancer Research (2022)

Abstract Colorectal cancer (CRC) is the second leading cause of cancer related deaths in the United States. This is largely due to metastasis, tumor relapse, and the vast heterogeneity of CRC tumors leading to treatment failure. Cancer stem cells (CSCs) are a small population of tumor-initiating cells thought to act as immortal seeds that can form metastases and contribute to tumor relapse. CSCs have been shown to exhibit plasticity or the ability to transition between differentiated and undifferentiated states to evade treatment and to promote tumor progression. Epiregulin (EREG) is an EGFR family ligand that is highly expressed in both states, as well as in treatment resistant CRCs of various mutation statuses. We showed that knock-out of EREG in a CRC cell line resulted in significant tumor inhibition in vivo, suggesting EREG is a promising target for therapeutic development. Therefore, we generated EREG-targeted antibody-drug conjugates (ADCs) to act as guided missiles for the delivery of cytotoxic drugs into EREG-expressing tumors to overcome plasticity and resistance in CRC. To develop a novel EREG ADC, we cloned and produced three separate EREG monoclonal antibody (mAbs) and tested them for binding, the ability to internalize into CRC cells, and to neutralize EREG activity. All three EREG mAbs were shown to bind with high affinity to EREG tethered to the surface of CRC cells and internalize to the lysosome, which is important for processing the release of drug from the ADC. We then conjugated the highest affinity EREG mAb and a non-targeting isotype control antibody to a highly cytotoxic drug via a cleavable peptide linker. EREG ADCs were evaluated in vitro against a wide panel of CRC cell lines of various Kras, Braf, and PI3CKA mutational statuses and different levels of EREG expression. Drug efficacy was determined using cytotoxicity assays to measure changes in CRC cell survival with escalating doses of unconjugated control antibody and EREG mAb, as well as control ADC (cADC) and EREG ADC. EREG mAb alone did not result in significant CRC cell death. However, EREG ADCs exhibited potent cell-killing in EREG-expressing CRC cells, whereas minimal effects were observed with cADC. Future progress will involve testing the safety and efficacy of EREG ADCs against patient-derived tumor xenograft models of CRC in vivo. These preliminary results demonstrate the therapeutic potential of EREG ADCs for targeting plasticity and drug resistance in CRC. Citation Format: Joan Jacob, Zhengdong Liang, Kendra Carmon. Development and characterization of an epiregulin antibody-drug conjugate for targeting colorectal cancer cell plasticity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4251.
Abstract 99: Interplay between CDK5 and IRF2BP1 enhances breast cancer brain metastasis
Authors: Arseniy E. Yuzhalin, Frank Lowery, Yohei Saito, Patrick Zhang, Dihua Yu
Journal: Cancer Research (2022)

Abstract Prognosis of patients with breast cancer brain metastasis is poor due to unavailability of effective treatments. Hence, more fundamental research is needed to broaden our understanding of mechanisms underlying the origin and development of brain metastasis. We have identified that expression of cyclin-dependent kinase 5 (CDK5) in cancer cells promotes brain metastasis growth in experimental mouse models through suppressing the antitumor immunity. Here, we interrogated the underlying mechanism that connects CDK5 with defective antitumor immunity. To understand the repertoire of CDK5 phosphorylation targets, we performed a quantitative stable isotope labeling by amino acids in cell culture (SILAC) phopshoproteomics analysis of cultured brain-seeking cell lines that have been genetically engineered to express shRNA targeting the CDK5 gene. The knockdown of CDK5 resulted in a dramatic dephosphorylation of multiple proteins, among which Interferon Regulatory Factor 2 Binding Protein 1 (Irf2bp1) is well recognized to function in mediating the immune response. Knockdown of CDK5 reduced the phosphorylation of Irf2bp1 at Ser66 in both 4T1 and T11 cells (Log10 fold change: -0.51 and -0.39, respectively, P less than 0.0001). These findings were further validated by co-immunoprecipitation of Irf2bp1 in cell lysates from shCtl and shCDK5 brain-seeking cancer cell lines, followed by immunoblotting for phosphoserine. Furthermore, analysis of Irf2bp1 protein band shifts and intensities using Phos-tag™ gels also demonstrated that CDK5 knockdown reduces the Irf2bp1 phosphorylation. In order to investigate the function of Irf2bp1, we established a stable knockdown of the Irf2bp1 gene in brain metastasis-derived cell lines 4T1.Br3 and T11.Br1. We observed that Irf2bp1-knockdown cells displayed a reduced expression of genes encoding the class I major histocompatibility complex (MHC-I) as well as Nlrc5, a key transcriptional regulator of MHC I. Thus, these findings indicate that CDK5 may regulate the expression of surface MHC-I in breast cancer brain metastasis cells through Irf2bp1 phosphorylation at Ser66, in the absence of Interferon gamma or other classically recognized MHC-I agonists. These findings reveal a previously unknown mechanism of MHC-I regulation in cancer cells, that might improve our knowledge about cancer cell immune evasion through MHC-I loss. Citation Format: Arseniy E. Yuzhalin, Frank Lowery, Yohei Saito, Patrick Zhang, Dihua Yu. Interplay between CDK5 and IRF2BP1 enhances breast cancer brain metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 99.
Abstract 3143: RIG-I agonism promotes immune activation in syngeneic tumor model
Authors: Mark Zielstorff, Yiping Chen, Jeremy Presland, Alan Byford, Amy Doty, Erik Munsell, Craig Parish, Gretchen Baltus, Lily Moy, George Addona, Jie Zhang-Hoover
Journal: Cancer Research (2022)

Abstract Activation of retinoic acid-inducible gene I (RIG-I) increases pro-inflammatory cytokine production, enhances antigen presentation, and promotes tumor cell apoptosis. Here we assessed the pharmacological activity of a RIG-I agonist encapsulated in lipid nanoparticle in the B16F10 mouse syngeneic tumor model. To probe whether additional pathways may complement RIG-I agonism, we tested our compound in combination with anti-PD-1 and anti-CTLA-4 immune checkpoint inhibitors. The RIG-I agonist was administered intratumorally (IT) in B16F10 tumors. In one arm, tumors were collected four hours post treatment for cytokine analysis. In a separate arm, tumor size was measured twice a week for two weeks to assess efficacy. To understand the mechanism of action of the RIG-I agonist, high dimensional phenotyping of dissociated tumors collected at various time points was evaluated using CyTOF. Tumor-specific memory T cell response was evaluated by tumor re-challenge in vivo. Intra-tumoral dosing of the RIG-I agonist generated robust and dose-dependent production of type I IFN in the tumor that led to tumor efficacy in B16F10 model. Within 24 hours of the RIG-I agonist administration tumor infiltrating myeloid cells, NK cells, and T cells showed upregulation of activation markers such as CD69, CCR7, and Ki-67, and MHC I and PD-L1 were upregulated on CD45- cells. On day 10 of the treatment, the number of CD8+ T cells and NK cells in the tumor and their expression of granzyme B increased substantially. The RIG-I agonist dosed in combination with anti-PD-1 and anti-CTLA-4 monoclonal antibodies enhanced B16F10 tumor killing, including complete tumor regressions. No tumor growth was observed when these mice were re-inoculated with B16F10 cells. In conclusion, the RIG-I agonist encapsulated in lipid nanoparticle activates tumor infiltrating immune cells, promotes tumor killing, and combines favorably with anti-PD-1 and anti-CTLA-4 antibodies. Citation Format: Mark Zielstorff, Yiping Chen, Jeremy Presland, Alan Byford, Amy Doty, Erik Munsell, Craig Parish, Gretchen Baltus, Lily Moy, George Addona, Jie Zhang-Hoover. RIG-I agonism promotes immune activation in syngeneic tumor model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3143.
Association of Medicaid Expansion With Emergency Department Visits by Medical Urgency
Authors: Theodoros V. Giannouchos, Benjamin Ukert, Christina Andrews
Journal: JAMA Network Open (2022)

Relatively little is known about the association of the Medicaid eligibility expansion under the Patient Protection and Affordable Care Act with emergency department (ED) visits categorized by medical urgency.To estimate the association between state Medicaid expansions and ED visits by the urgency of presenting conditions.This cross-sectional study used the Healthcare Cost and Utilization Project State Emergency Department Databases from January 2011 to December 2017 for 2 states that expanded Medicaid in 2014 (New York and Massachusetts) and 2 states that did not (Florida and Georgia). Difference-in-differences regression models were used to estimate the changes in ED visits overall and further stratified by the urgency of the conditions using an updated version of the New York University ED algorithm between the states that expanded Medicaid and those that did not, before and after the expansion. Data were analyzed between June 7 and December 12, 2021.State-level Medicaid eligibility expansion.Emergency department visits per 1000 population overall and stratified by medical urgency of the conditions.In total, 80.6 million ED visits by 26.0 million individuals were analyzed. Emergency department visits were concentrated among women (59.3%), non-Hispanic Black individuals (28.3%), non-Hispanic White individuals (47.8%), and those aged 18 to 34 years (47.5%) and 35 to 44 years (20.4%). The rates of ED visits increased by a mean of 2.4 visits in nonexpansion states and decreased by a mean of 2.2 visits in expansion states after 2014, resulting in a significant regression-adjusted decrease of 4.7 visits per 1000 population (95% CI, -7.7 to -1.5; P = .003) in expansion states. Most of this decrease was associated with decreases in ED visits by conditions classified as not emergent (-1.5 visits; 95% CI, -2.4 to -0.7; P < .001), primary care treatable (-1.1 visits; 95% CI, -1.6 to -0.5; P < .001), and potentially preventable (-0.3 visits; 95% CI, -0.5 to -0.1; P = .02). No significant changes were observed for ED visits related to injuries and conditions classified as not preventable (-1.4; 95% CI, -3.1 to 0.3; P = .10), as well as for substance use and mental health disorders (0.0; 95% CI, -0.2 to 0.2; P = .94).The findings of this study suggest that Medicaid expansion was associated with decreases in ED visits, for which decreases in ED visits for less medically emergent ED conditions may have been a factor.
Abstract 58: Novel enzymatic fragmentation for challenging samples and methods
Authors: Brittany S. Sexton, Maggie Heider, Louise Williams, Bradley Langhorst, Eileen Dimalanta, Lynne Apone
Journal: Cancer Research (2022)

Abstract Next Generation Sequencing (NGS) requires fragmentation of DNA molecules upstream of sequencing. Current methods for fragmentation include mechanical shearing and enzymatic fragmentation for NGS library preparation. Mechanical shearing requires costly instruments, can be difficult to automate for high throughput labs, and results in sample loss. In comparison, enzymatic fragmentation methods do not require expensive instruments and are automation friendly. However, current enzymatic fragmentation methods on the market can remove DNA modifications such as methylation, cement DNA damage resulting from formalin fixation in final libraries and can introduce sequencing artifacts or bias. Therefore, while many fragmentation methods are commercially available, challenges remain for sequencing samples such as FFPE DNA or for detecting DNA modification (e.g., 5-methylcytosine). We have developed a novel enzymatic fragmentation method that can be used upstream of library preparation for DNA methylation assessment or FFPE DNA. The novel enzymatic fragmentation method is quick and robust, taking as little as 20 minutes. It is automation-friendly and can be used to generate DNA fragments ranging from as small as 50 bp up to over 1000 bp. Here we demonstrate the use of the novel enzymatic fragmentation method upstream of 5mC library preparation methods. This fragmentation method maintained the methylation marks. These libraries showed improvements in GC bias, library yield, library complexity and other sequencing metrics over libraries generated with mechanically sheared DNA. The use of the novel enzymatic fragmentation method with FFPE DNA library preparation resulted in improvements in sequencing metrics (increased proper pairs, etc.). There was reduced FFPE-damage-derived mutations compared to mechanical shearing or other enzymatic fragmentation methods. Fragmenting DNA to defined sizes for diverse applications and sample types remains a challenging aspect of NGS library preparation. This new, robust enzymatic fragmentation method overcomes the limitations of some traditional mechanical and enzymatic fragmentation methods and improves the library preparation and sequencing for both DNA modification assessment studies and FFPE DNA. Citation Format: Brittany S. Sexton, Maggie Heider, Louise Williams, Bradley Langhorst, Eileen Dimalanta, Lynne Apone. Novel enzymatic fragmentation for challenging samples and methods [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 58.
Abstract 5254: Association of USP6 mutation with tumor mutation burden and survival in melanoma patients treated with immune checkpoint inhibitors
Authors: De Long, Dandan Fan, Yaoxu Chen, Mengli Huang
Journal: Cancer Research (2022)

Abstract Background: Melanoma is a serious skin cancer. Immune checkpoint inhibitors (ICIs) including pembrolizumab, nivolumab, ipilimumab have been approved by FDA. However, ICIs demonstrate antitumor effects only in a fraction of patients and research exploring the association between gene mutation and clinical benefit is limited. USP6 (Ubiquitin-specific protease 6) mutation rate is high in melanoma. Studies have shown that USP6 functions as a tumor suppressor in Ewing Sarcoma through the activation of NK cells and macrophages, which indicates that USP6 activity may create a "hot" tumor microenvironment in immunotherapy. The association between USP6 mutation and survival in melanoma is unknown. Methods: The association between USP6 mutation with TMB and survival data was analyzed in melanoma patients from the public immunotherapy-treated cohort called Melanoma.Allen2015.WES.110, which worked as training cohort while another cohort called Melanoma.Hugo2016.WES.38 worked as validation cohort. Wilcoxon test was used for the comparison of TMB. OS (Overall survival) analysis were conducted in the public cohort using Kaplan-Meier curves and log-rank tests. In addition, the genomic and immune cell infiltration data of 466 patients with Skin Cutaneous Melanoma was obtained from TCGA and the correlation analysis was further analyzed by CIBERSORT. Statistical significance was set at p=0.05. Results: In the training cohort, 10.9% (12/110) melanoma patients harbored USP6 mutation. USP6 mutation is associated with higher TMB (p=0.0007) and results in significantly longer OS (21.3 vs 8.1 months; HR, 0.44; p=0.049).Meanwhile, the validation cohort shows that USP6 mutation results in higher TMB without significant difference (p=0.08) and significantly longer OS (31.5 vs 14.4 months; HR, 0.14; p=0.0026).Furthermore, the correlation analysis between immune infiltration and USP6 mutation status in melanoma shows that both M1 macrophages and follicular helper T cells increased significantly (p=0.02, p=0.033), while differential neutrophil decreased significantly (p=0.048). Conclusions: This study shows that USP6 mutation may serve as a potential positive biomarker of ICIs in melanoma since it correlated with higher TMB, the up regulation of M1 macrophages, follicular helper T cells and the down regulation of differential neutrophil. Citation Format: De Long, Dandan Fan, Yaoxu Chen, Mengli Huang. Association of USP6 mutation with tumor mutation burden and survival in melanoma patients treated with immune checkpoint inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5254.
Abstract 3183: Targeting a myofibroblastic prostate cancer-associated fibroblast subtype through pharmacological inhibition of NADPH oxidase 4
Authors: Elena Brunner, Lucy Neumann, Elisabeth Damisch, Martin Puhr, Georg Schäfer, Cédric Szyndralewiez, Helmut Klocker, Natalie Sampson
Journal: Cancer Research (2022)

Abstract Recent developments in single cell sequencing have revealed significant heterogeneity in the stromal tumor microenvironment. It is now widely accepted that there are different cancer-associated fibroblast (CAF) subtypes with different functions and effects on tumor progression. Since CAFs are generally considered an emerging therapeutic target, it is crucial to identify those subtypes that are tumor-promoting and to characterize their driver pathways. In this study we describe a population of CAFs in prostate cancer (PCa) that express elevated levels of NADPH oxidase 4 (Nox4) and localize adjacent to tumor foci. We previously showed that Nox4 is essential for TGFβ-mediated differentiation to a myofibroblastic CAF phenotype and that its increased expression is associated with biochemical relapse and reduced survival. Thus, this study aims to investigate whether pharmacological Nox4 inhibition can be used as an adjuvant therapeutic approach in PCa and which molecular pathways are regulated by Nox4 in the tumor microenvironment. Experiments using GKT831, a small molecule Nox1/Nox4 inhibitor with promising effects in clinical trials for fibrotic diseases, so far support its use as a therapeutic target. Most importantly, Nox4 inhibition reduced CAF marker expression in primary prostate CAFs and attenuated the expression of PSA, the key clinical biomarker of PCa progression, in ex vivo cultured human PCa tissue. The translational application of Nox4 inhibition is currently under investigation in vivo using CAF-PCa cell xenografts. To elucidate the molecular mechanisms regulated by Nox4 we performed integrative bioinformatics and functional assays, which revealed that Nox4 regulates CAF adhesion and migration. In addition, we found that Nox4 regulated genes were associated with a YAP signature and the transcription factor TEAD1, a major cofactor of YAP. Ongoing experiments suggest that during adhesion Nox4 signals via oxidation of SHP2, a redox-sensitive phosphatase that has previously been implicated in regulating YAP transcriptional activity. Previous studies have shown that adhesion and mechanotransduction pathways are commonly altered in myofibroblastic CAFs and that they support the formation of a tumor-promoting microenvironment. Our data suggest that Nox4 acts as a central regulator of these key oncogenic pathways and thus represents a promising therapeutic target. Citation Format: Elena Brunner, Lucy Neumann, Elisabeth Damisch, Martin Puhr, Georg Schäfer, Cédric Szyndralewiez, Helmut Klocker, Natalie Sampson. Targeting a myofibroblastic prostate cancer-associated fibroblast subtype through pharmacological inhibition of NADPH oxidase 4 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3183.
Abstract 5070: Prostate-specific membrane antigen (PSMA) targeted multiplexed siRNA-mediated gene silencing of CD46 and PD-L1 in prostate cancer
Authors: Zhihang Chen, Balaji Krishnamachary, Yelena Mironchik, Sangeeta R. Banerjee, Martin G. Pomper, Zaver M. Bhujwalla
Journal: Cancer Research (2022)

Abstract Small interfering RNA are suitable for gene silencing through a sequence-specific RNA interference process. The redundancy and complexity of molecular pathways in cancer create a need for multiplexed targeting that can be achieved with multiplexed siRNA delivery. Here we delivered multiplexed siRNA with a PSMA-targeted biocompatible dextran nanoparticle (NP) to downregulate CD46 and PD-L1 siRNA in PSMA expressing prostate cancer cells. The multiplexed gene targets selected, PD-L1 and CD46, play important roles in the escape of cancer cells from immune surveillance. PSMA is abundantly expressed by prostate cancer cells allowing prostate cancer specific delivery of the NPs. The NP was decorated with acid cleavable amine functional groups through acetal bonds that undergo degradation under acidic conditions providing rapid release of siRNA. Cell imaging and flow cytometry studies confirmed PSMA-specific delivery of CD46 and PD-L1 siRNA to high PSMA expressing PC-3 PIP cells. Immunoblot, qRT-PCR and flow cytometry confirmed downregulation of CD46 and PD-L1 following treatment with multiplexed siRNA at a concentration of 50 nM. These studies pave the way for delivering multiplexed siRNA to tumors in vivo to unmask tumors to the immune system using PSMA targeted biocompatible NPs. Citation Format: Zhihang Chen, Balaji Krishnamachary, Yelena Mironchik, Sangeeta R. Banerjee, Martin G. Pomper, Zaver M. Bhujwalla. Prostate-specific membrane antigen (PSMA) targeted multiplexed siRNA-mediated gene silencing of CD46 and PD-L1 in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5070.